Biochip reader

ABSTRACT

The present invention provides a biochip reader for reading with a detector the fluorescence image information from genes to which fluorescent substances are stuck and which are poured into biochip cells, by emitting coherent light beams such as laser light onto the cells as excitation light. The present invention aims to achieve a biochip reader that is small, cheap, and highly durable.

BACKGROUND OF THE INVENTION

[0001] 1. Field of the Invention

[0002] The present invention relates to a biochip reader and, inparticular, to a biochip reader using light from a coherent source suchas laser as excitation light.

[0003] 2. Description of the Prior Art

[0004]FIG. 1 is a schematic view illustrating the principle andconfiguration of a biochip reader. This figure is based on the confocaloptical system, mentioned on pages 132 and 133 of “Application ofconfocal laser microscopes to medicine and biology,” New OpticalMicroscopes, Vol. II, published by Gakusai Kikaku (which means“Interdisciplinary Planning”) Co., Ltd. on Mar. 28, 1995. In a biochipreader based on such a schematic view illustrating its principle andconfiguration, laser light from light source 1 emitted through pinholesprovided in pinhole plate 2 is incident to objective lens 5 after beingcollimated by lens 3 and transmitted through dichroic mirror 4.Objective lens 5 condenses this excitation light and irradiates sample(biochip) 6.

[0005] The fluorescent substances stuck to genes on biochip 6 emitfluorescence by being excited with excitation light. This fluorescenceis reflected by dichroic mirror 4 after passing through objective lens 5and then concentrated by condenser lens 7 and forms image on the planeof pinhole plate 8. These images are the fluorescence images of genes onsample 6 and are detected by detector 9. To observe the fluorescenceimage of sample 6 surface (two-dimensional image), it is necessary toscan the sample 6 surface with excitation light. In this case, normally,the excitation light is not scanned but the stage on which sample 6 isplaced (not shown in the figure) is scanned in the directionperpendicular to the optical axis (called stage scan).

[0006] In such a biochip reader, laser light is used as the light sourcebecause use of white light as a source causes a shortage of lightquantity. In addition, employing the confocal type using pinholes notonly prevents the detected image from being affected by dust stuck tothe surface of sample 6, but also prevents speckle noise from beinggenerated because the excitation light is emitted to the sample afterbeing condensed.

[0007] However, in such conventional biochip readers, there are problemsthat adjustment or conditioning of pinholes is troublesome and also thisraises its cost. Furthermore, it is disadvantageous that the stage isrequired to be durable because it is moved for scanning and thus thecost of the stage becomes high.

[0008] Next, FIG. 2 shows another example of a schematic view of aconventional biochip reader illustrating its principle andconfiguration. Such a principle is, for example, mentioned on page 158of “GFP and Bio-imaging,” Experimental Chair in Post-genome Age, No. 3,a separate volume of Experimental Medicine, published by Yodosha Co.,Ltd. on Oct. 25, 2000.

[0009] In FIG. 2, excitation light from a parallel-light light sourcesuch as laser (not shown in the figure) is concentrated by condenserlens 7 and incident to objective lens 13 after being reflected bydichroic mirror 12. In this case, the excitation light forms an image inthe position of focal length f of objective lens 13 and this image actsas the second source to be incident to objective lens 13.

[0010] Sample 6 is irradiated with the excitation light that hastransmitted through objective lens 13. As a sample, for example, a DNAchip that contains DNA on a slide glass whose surface is flat, or thelike is used. At each site 15 of the DNA chip, fluorescent substanceswith which the DNA is labeled emit fluorescence by being excited withexcitation light. The fluorescence forms an image on detector 18 via theimage forming optical system. In other words, the fluorescence is madeparallel by objective lens 13 as shown with continuous lines, passesthrough dichroic mirror 12 and barrier filter 16, and is incident tolens 17. The image of sample 6 formed by lens 17 is detected by detector18.

[0011] In this case, the behavior of the excitation light irradiatingover the entire sample surface is as follows:

[0012] Excitation light reflected at the flat sample surface shown withbroken lines (this excitation light is called the reflected excitationlight or the return excitation light) is focused by objective lens 13and focused in the position of focal length f of objective lens 13. Theexcitation light is incident to detector 18 after passing through lens17 whose intermediate image plane is set at this focal position. Inaddition, the reflected excitation light is transmitted through dichroicmirror 12 and barrier filter 16 before passing through lens 17. Barrierfilter 16 is formed to pass fluorescence but reject (attenuate) thereflected excitation light and thus the reflected excitation light mixedinto detector 18 as background light is reduced by being passed throughthis barrier filter 16.

[0013] However, in such conventional microscopes, the reflectedexcitation light cannot be sufficiently reduced although it isattenuated with the barrier filter. Although background light must bereduced to approximately 10⁻⁹ of the fluorescence to be detected in themeasurement of fluorescent molecules or the like, there is a problemthat an attenuation factor (ratio of exit light intensity to incidentlight intensity) of only about 10⁻⁷ can be obtained in this reader.Thus, the attenuation is clearly not sufficient.

[0014] Further, FIG. 3 is a schematic view of the biochip reader using amicrolens array system illustrating its principle and configuration,mentioned in the Japanese patent application No. 2001-2264 submitted bythe applicant concerned. In FIG. 3, a plurality of microlenses ML isarranged on microlens array 21, and light that has passed through eachmicrolens (excitation light) is emitted to sample 23 through dichroicmirror 22. Sample 23 is a biochip, into each of whose cells genes arepoured, each cell being arranged at the same pitch as the abovemicrolenses and thus spatially arranged so that excitation light fromeach microlens irradiates each cell respectively.

[0015] Fluorescent substances are stuck to each gene on the biochip andgenerate emission owing to irradiation of excitation light. The emittedfluorescence is reflected by dichroic mirror 22, incident to lens 25through barrier filter 24, and forms an image on detector 26 (e.g. acamera). In such a manner, a fluorescence image of the biochip can beobserved with camera 26.

[0016] In addition, barrier filter 24 acts to transmit fluorescence butreject excitation light, and thus the use of this filter can prevent theexcitation light reflected by the surface of sample 23 from beingincident to camera 26.

[0017] However, in such conventional biochip readers, if shading(cone-shaped light intensity distribution) is included in excitationlight from the light source, non-uniformity is generated in read data.To prevent this, it is suggested to make the ratio a of the minimumvalue of light intensity to its maximum value 10 to 20%, by making theamount of shading small using only a center portion of the above conicalintensity distribution as shown in FIG. 3. However, there occurs anotherproblem that much light is wasted (the light-utilizing efficiencydeteriorates) because this method discards light in the peripheralportion.

[0018] Furthermore, if the expression of mRNA in a biochip is to bemeasured using cDNA, there are large differences in the amounts ofexpression, which causes problems such as cases where a 10- to 100-folddifference exists as shown in FIG. 4(b) between the expression (signalintensity) of gene A and that of gene B shown in FIG. 4(a). That is, ifthe amount of expression is to be measured precisely without giving anychange, analog-to-digital converters and amplifiers used in the detectormust have wide dynamic ranges and high accuracy, and so are expensive.This is a problem.

[0019] In addition, there is another problem that, although there is amethod to measure the amount of expression several times by changing thegains of analog-to-digital converters and amplifiers, this method takestime for measurement, and dispersion in measured values and discoloringof biochips also increase.

SUMMARY OF THE INVENTION

[0020] The objective of the present invention is to solve the aboveproblems and to provide a biochip reader that is small, cheap and highlydurable.

[0021] Another objective of the present invention is to provide abiochip reader that can sufficiently attenuate the reflected excitationlight that constitutes background light.

[0022] A further objective of the present invention is to provide abiochip reader that can raise the light-utilization efficiency and canmeasure samples with high accuracy even if cheap and moderately accurateanalog-to-digital converters and amplifiers are used.

BRIEF DESCRIPTION OF THE DRAWINGS

[0023]FIG. 1 is a schematic view of a conventional biochip readerillustrating its principle and configuration.

[0024]FIG. 2 shows another example of a schematic view of a conventionalbiochip reader illustrating its principle and configuration.

[0025]FIG. 3 shows the third example of a schematic view of aconventional biochip reader illustrating its principle andconfiguration.

[0026]FIG. 4 is a drawing illustrating a biochip and a differencebetween the amounts of expression (signal intensities) for genes.

[0027]FIG. 5 shows a schematic view indicating the configuration of anessential part of an embodiment for a biochip reader based on thepresent invention.

[0028]FIG. 6 shows a schematic view indicating the configuration of, anessential part of another embodiment of the present invention.

[0029]FIG. 7 shows a schematic view indicating the configuration of anessential part of-the third embodiment of the present invention.

[0030]FIG. 8 is a graph indicating the attenuation factor characteristicof the barrier filter.

[0031]FIG. 9 shows a schematic view indicating the configuration of anessential part of another embodiment of a biochip reader based on thepresent invention.

[0032]FIG. 10 shows a schematic view illustrating a biochip reader usinga light source array.

[0033]FIG. 11 shows a schematic view indicating another embodiment of animage-forming lens.

[0034]FIG. 12 shows a schematic view indicating a biochip reader using amask.

[0035]FIG. 13 shows a schematic view indicating a biochip readerconfiguration using a mirror.

[0036]FIG. 14 shows a schematic view indicating the configuration of anembodiment for a transmission type biochip reader.

[0037]FIG. 15 shows a schematic view indicating the configuration of anessential part of another embodiment of the present invention.

[0038]FIG. 16 shows a schematic view indicating the configuration of anessential part of the third embodiment of the present invention.

[0039]FIG. 17 is a drawing illustrating a condition of gene arrangementon a sample.

[0040]FIG. 18 shows a schematic view indicating the configuration of anessential part of the other embodiment of the present invention.

[0041]FIG. 19 shows a schematic view indicating the configuration of anessential part of the separate other embodiment of the presentinvention.

[0042]FIG. 20 is a graph showing the input-output characteristic ofdetector elements.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0043] The present invention will be described below in detail withreference to the drawings. FIG. 5 shows a schematic view indicating theconfiguration of an essential part of an embodiment for a biochip readerbased on the present invention. In FIG. 5, numeral 31 shows a lightsource generating coherent light such as laser light (hereafter called“laser light”) as excitation light, numeral 32 shows a lens convertingthe laser light into parallel light and numeral 33, a microlens array.Microlens array 33 is mounted on rotation plate 34 and composed of aplurality of microlenses ML arranged on that plate.

[0044] Numeral 35 shows a motor for rotating rotation plate 34, numeral36 a sample, numeral 37 a lens, numeral 38 a barrier filter, numeral 39a condenser lens, and numeral 40 a camera using CCDs or the like asdetector elements.

[0045] Laser light emitted from light source 31 is changed to parallellight by lens 32 and is incident to microlens array 33. Each microlensML irradiates sample 36 respectively by condensing laser light. Sample36 has a construction in which a plurality of cells is arranged in atwo-dimensional manner and genes are poured into each cell.

[0046] When rotation plate 34 is rotated with motor 35, excitation lightbeams focused with each microlens ML are scanned over sample 36.Microlenses ML are arranged on rotation plate 34, with the relationbetween spatial positions such that each excitation light beam can bescanned over each cell individually.

[0047] Fluorescence from each gene is incident to lens 39 throughbarrier filter 38 after being incident to lens 37. Barrier filter 38acts to transmit fluorescence from sample 36 but reduces the incidentexcitation light passing through sample 36 and thus is used to rejectbackground light for the sample image.

[0048] The sample image focused and formed by lens 39 is detected bydetector elements (not shown in the figure) of camera 40.

[0049] Using such a configuration, a two-dimensional sample image can beeasily obtained by producing multi-beams using a plurality ofmicrolenses and by scanning samples with those beams.

[0050] In addition, it is not necessary to employ a confocal reader asrequired in conventional readers, because dust stuck to samples can bedrastically reduced by using cartridges or the like. However, anadequate quantity of excitation light is required. In the presentinvention, since laser light is used as excitation light, a sufficientquantity of light at high luminance can be obtained.

[0051] Further, speckle noise is not generated in a sample image in thepresent invention, because the excitation light is focused withmicrolenses. Furthermore, since pinholes as in the case in conventionalreaders are not used, readers based on the present invention are easierto adjust. In addition, readers that are small, cheap and highly durablecan be easily obtained because the moving mechanism to move a stage isnot necessary.

[0052]FIG. 6 shows a schematic view indicating the configuration of anessential part of another embodiment of the present invention. Althoughthe biochip reader shown in FIG. 5 is of the transmission type., thereader shown in FIG. 6 is of the reflection type. Dichroic mirror 41 isarranged between microlens array 33 and sample 36 and fluorescenceemitted from sample 36 is reflected by this dichroic mirror 41 andincident to lens 39. Lens 39 condenses this fluorescence and forms animage on the detector element plane of camera 40. Other configurationsand operations are the same as those shown in FIG. 5.

[0053] The above embodiments of the present invention have the followingeffects:

[0054] (1) Since excitation light beams irradiating each gene on asample are focused with microlenses, speckle noise is not generated onobserved images of the genes.

[0055] (2) There are fewer adjusting points than in conventionalconfocal biochip readers and thus fabrication is easier because thereader is not of the confocal type and so does not use pinholes.

[0056] (3) The reader does not require the stage on which a sample isplaced for light scanning to be moved as in conventional readers. Thisfacilitates the production of small, cheap, and highly durable biochipreaders.

[0057]FIG. 7 shows another embodiment of the present invention, in whichexcitation light is incident to a barrier filter at the incident angleof ±5 degrees or less. The difference of this embodiment from theexample of conventional ones shown in FIG. 2 is the arranged barrierfilter position. In FIG. 7, barrier filter 16 is arranged between lens17 and detector 18. The attenuation factor (ratio of exit lightintensity to incident light intensity) of barrier filter 16 depends onthe incident angle of light as shown in FIG. 8. In order to obtain theattenuation factor of 10⁻⁷ or better, it is necessary to suppress theincident angle to the barrier filter to ±5 degrees or less, while thedata shown in FIG. 8 are example measurements for a barrier filter usingparallel laser light. In general-purpose spectrophotometers, thesevalues cannot be obtained because divergent or convergent light is used.Such arrangement of barrier filter 16 attenuates the incident excitationlight to a value of about 10⁻⁹ of the original incident light becausethe excitation light is incident to barrier filter 16 at an angle of ±5degrees or less. For this reason, background light at an observed imageon the surface of detector 18 is sufficiently little.

[0058] In addition, the present invention is not limited to the aboveembodiments. For example, configurations illustrated below may beemployed.

[0059] (1) The Case Related to the Size of Light Source Image:

[0060]FIG. 9 shows a schematic view indicating the configuration of anessential part of Koehler's illumination system in the case wherenon-laser light such as white light is used. Light from light source 51(diameter of light source is “a”) forms second light source 52 havingdiameter a′ by being incident to condenser lens 11. Sample 14 isirradiated by this second light source 52. The angle β of the angle ofexcitation light irradiating sample 14 in this case (this angle iscalled “irradiation angle”) depends on the diameter of second lightsource 52.

[0061] In transmission type or reflection type microscopes, necessaryand sufficient resolution cannot be obtained unless there is a largeangle β in Koehler's illumination. Similarly, in fluorescencemicroscopes, the diameter a′ of light source image 52 is expanded toabout 10 times the diameter “a” of the original light source 51,enlarging the angle However, since, when the angle β is made large, theincident angle to barrier filter 16 also becomes large and degrades theattenuation factor of excitation light, there is a limit for angle β.The following relationship exists between the light source image and thefocal length f of objective lens 13:

a′/2=fβ

[0062] That is,

β=a′/(2f)

[0063] where f is the focal length of objective lens 13.

[0064] In order to obtain a sufficient attenuation factor, it isnecessary to suppress the angle β to ±5 degrees or less. To achievethis, for example, the size of the light source or the focal length f′of an optical system for excitation or the like may be adjusted.

[0065] (2) The Case of Light Source Array:

[0066]FIG. 10 shows a schematic view illustrating the configuration ofthe reader using a light source array composed of two differentwavelength light sources such as green G and red R. The G light sourceis placed on the optical axis in a position f′ apart from lens 11 andthe R light source is placed in a place apart from the optical axis by bin that position. In such arrangement, light from the G light source isincident normal to the surface of a sample placed horizontally and lightfrom the other R light source is incident to that surface at anirradiation angle of γ(=f′b).

[0067] The excitation light reflected at the sample surface istransmitted through objective lens 13 and dichroic mirror 12. Then,shorter wavelength light (on the G light source side) is reflected bysecond dichroic mirror 12 a and the other longer wavelength light (onthe R light source side) is transmitted through second dichroic mirror12 a.

[0068] The former forms an image on detector 18 via image-forming lens17 and barrier filter 16 and the latter forms an image on detector 18 avia image-forming lens 17 a and barrier filter 16 a.

[0069] In this case, if barrier filter 16 a is mounted horizontally,reflected excitation light originated by the R light source is obliquelyincident to the filter at an angle of γ. Accordingly, barrier filter 16a is arranged at angle γ oblique to the horizontal plane so that theexcitation light is incident normal to the plane.

[0070] This makes it possible for the excitation light reflected fromthe sample surface to be incident normal to barrier filters 16 and 16 aand thus both of the excitation lights are sufficiently attenuated.

[0071] (3) Example of Version Related to Image-Forming Lens:

[0072]FIG. 11 shows a schematic view indicating the configuration ofessential parts of an image-forming lens. This is an example for using alens with a fluorescence filter 60 that has the barrier filter functiontogether with the image-forming lens function.

[0073] This lens with a fluorescence filter 60 has a construction inwhich an interfering filter for fluorescence 62 is stuck to the flatside of convex lens 61, and attenuates the reflected excitation lightwith this interfering filter 62 like the barrier filter.

[0074] (4) Example of Version for Changing to the point Mask Type:

[0075] As shown in FIG. 12, the excitation light reflected from thesample is cut by placing mask 71 in the position where the excitationlight is focused by objective lens 13. Mask 71 is, for example,supported with a transparent plate or three stays or the like radiallyextended in the horizontal direction. If the diameter Φ of mask 71 isabout 1.22 λ/NA, (in other words, if the opening of mask 71 has an areanearly equal to that for the diameter of the excitation light beam), thereflected excitation light can be cut by 80% or more. In this case, λdenotes the wavelength of excitation light and NA represents theNumerical Apertures for objective lens 13. The barrier filters used inthe above embodiments need not be used. Otherwise, a cheap filter thathas low attenuation factor may be used.

[0076] (5) Example of Version for Changing to the Point Mirror Type:

[0077] In lieu of the dichroic mirror shown in the above embodiments, asmall piece of mirror 72 can be placed in the position of the secondlight source in Koehler's illumination as shown in FIG. 13. This mirror72 has an area nearly equal to that for the diameter of excitation lightbeam and reflects the excitation light from light source 81 like thedichroic mirror and irradiates sample 14. At the same time the mirroralso reflects the reflected excitation light focused with objective lens13 towards the light source. Accordingly, the reflected excitation lightis not incident to the detector (not shown in the figure).

[0078] In addition, mirror 72 is held by support 73 composed of atransparent substrate or stays to keep its mounting position and angle.

[0079] (6) The Case Using a Transmission Type Fluorescence Reader:

[0080]FIG. 14 shows a schematic view indicating an embodiment for atransmission type fluorescence reader. In this case, the transmittedexcitation light can also be attenuated using the barrier filtersimilarly. Barrier filters 94 and 97 are arranged between sample 93 andobjective lens 95 and between image-forming lens 96 and detector 18respectively. In this case, either of the barrier filters only may beemployed.

[0081] In addition, objective lens 95 and image-forming lens 96constitutes a telecentric system.

[0082]FIG. 15 shows that barrier filter 38 is arranged between lens 39and camera 40 in the configuration shown in FIG. 5. The excitation lighttransmitted through sample 36, as shown with dotted lines in FIG. 15, isincident to an image-forming optical system composed of lenses 37 and 39as almost parallel light and then incident to camera 40 as almostparallel light.

[0083] In this case, the excitation light is incident to barrier filter38 at an incident angle of ±5 degrees or less and is attenuated to 10⁻⁷or less of the incident light.

[0084] According to these embodiments, the following effects can berecognized:

[0085] (1) The excitation light can easily be attenuated because theexcitation light is devised to be incident to the barrier filter at anincident angle of ±5 degrees or less.

[0086] (2) Actions equivalent to using a barrier filter can easily beachieved without using a barrier filter by employing a convex lens asthe image-forming lens and attaching an interfering filter forfluorescence to the convex lens.

[0087] (3) Mixing the reflected excitation light into the detector caneasily be prevented without using the barrier filter because thereflected excitation light focused with the objective lens is masked orreflected.

[0088] (4) The excitation light to be incident to the detector caneasily be attenuated by arranging the barrier filter(s) even intransmission-type fluorescence readers.

[0089] In addition, as a solution to the problems shown in FIG. 3 andFIG. 4 indicating conventional examples, the following configurationshould be adopted:

[0090] At the same time as generating excitation light composed ofstrong and weak light intensity parts from a light source, theexcitation light is intentionally shaded to a significant extent. Forexample, as shown in FIG. 16, the excitation light is forced to have alight intensity pattern in which the intensity is strong at the centerpart and weak in the peripheral part. The light intensity pattern isarranged such that the ratio a of the lowest value to the highest valueof light intensity I in the effective range R of that parallel light isabout 90%. The excitation light having such a light intensitydistribution irradiates sample 23 in the same light intensity patternvia microlens array 21 and dichroic mirror 22.

[0091] On the other hand, at sample 23, genes are arranged so that theexpression distribution shows an inverted pattern from the intensitypattern of excitation light. This is done by arranging the genes withthe higher expression genes placed in outer cells and the lowerexpression genes placed in inner cells, as shown in FIG. 17.

[0092] By placing the light intensity distribution of excitation lightand the expression distribution of genes in a relationship as mentionedabove, low and high expression genes, in other words, genes whichproduce little fluorescence or much fluorescence, are irradiated withstrong and weak intensity excitation light respectively.

[0093] As a result, even if there is a great difference in expressions,the difference in the fluorescence from each gene to be incident to thedetector is small. Accordingly, analog-to-digital converters andamplifiers that are cheap and have moderate accuracy can be used in thedetector because wide dynamic ranges and high accuracy are not required.

[0094] Further, the excitation light distribution is separately measuredin advance and fluorescence from the sample is used by being correctedusing the excitation light distribution.

[0095] Furthermore, the present invention is not limited to the aboveembodiments. For example, if only a part of excitation light is employedusing light cutting or light reducing mask 100 as shown in FIG. 18, theexcitation light emitted to a biochip indicates the light intensitydistribution shown in the figure. As described above, if a mask havingthe light cutting or light reducing pattern (also called “concentrationpattern” here) is used, the degree of freedom in arranging genes on abiochip is greatly improved.

[0096] In addition, the reader can also be configured so as to makeshading of excitation light variable as shown in FIG. 19. In FIG. 19,the difference of the configuration from that shown in FIG. 16 is thezoom mechanism. Zoom mechanism 110 uses ordinary zoom lenses andproduces a parallel light beam from the light source (not shown in thefigure) to microlens array 21 after suitably expanding or contractingthe light beam.

[0097] If the beam is expanded with zoom mechanism 110, the lightintensity distribution pattern of the excitation light emitted from thelight source is extended transversely, and so the intensity distributionpattern of excitation light incident to microlens array 21 becomesflatter. On the contrary, if the light intensity distribution pattern iscontracted, the incident excitation light distribution gives a steeperpattern.

[0098] Since shading varies with expansion or contraction as shownabove, shading can be set arbitrarily corresponding to sample 23 byoperating zoom mechanism 110.

[0099] Further, a configuration to detect a fluorescence image using adetector composed of detector elements having input-outputcharacteristics of a logarithmic relationship as shown in FIG. 20 may beused without changing the light intensity distribution of excitationlight or the arrangement of sample genes.

[0100] According to such a configuration, even if there is a greatdifference in inputs (fluorescence quantities), saturation inanalog-to-digital converters and amplifiers on the detector side can beprevented and so such converters and amplifiers do not need wide dynamicranges and high accuracy.

[0101] In accordance with the invention having the embodiments describedabove, even if there are great differences in the expressions of eachgene on a biochip, wide dynamic ranges and high accuracy are notrequired for detectors. Thus, satisfactory sample images can be detectedwith a detector using analog-to-digital converters and amplifiers thatare cheap and have moderate accuracy.

[0102] Furthermore, since shading for light intensity distribution ofthe light source can be increased, obtaining a great increase in theefficiency of light quantity can also be intended.

What is claimed is:
 1. A biochip reader that reads fluorescencegenerated from genes of each of its cells by irradiating each cell withcoherent light such as laser light as the excitation light; comprising arotation plate formed so as to be rotatable, on which a plurality ofmicrolenses is arranged, and a two-dimensional detector that detects afluorescence image of said biochip using detector elements arranged in atwo-dimensional manner; further configured to rotate said rotationplate, to scan said biochip with light using excitation light beamsindividually condensed with a said plurality of microlenses, and toindividually irradiate each cell.
 2. A biochip reader in accordance withclaim 1, which is of the transmission type or the reflection type.
 3. Abiochip reader, configured to irradiate a sample whose surface is flatwith excitation light, to form images of fluorescence generated fromfluorescent substances in the sample via an image-forming opticalsystem, and to read the images with a detector; wherein a barrier filterwhich acts to transmit fluorescence from said sample surface but toattenuate excitation light reflected from said sample is arranged insaid image-forming optical system so that excitation light reflectedfrom said sample is incident to the barrier filter at an incident angleof ±5 degrees or less.
 4. A biochip reader in accordance with claim 3,wherein said barrier filter is arranged between the image-forming lensin said image-forming optical system and said detector to detect imagesformed with this image-forming lens.
 5. A biochip reader in accordancewith claim 3, wherein the irradiation angle of excitation light based onthe light source in Koehler's illumination is configured to be ±5degrees or less.
 6. A biochip reader in accordance with claim 3 or claim4, wherein, if a sample is irradiated using a light source arraygenerating a plurality of excitation light beams whose wavelengths aredifferent from each other, the barrier filter, to which the reflectedexcitation light is incident, based on excitation light that is incidentto a sample at an incident angle γ, is arranged oblique to said samplesurface at angle γ.
 7. A biochip reader configured to irradiateexcitation light to a sample, to form an image of fluorescence generatedfrom fluorescent substances in said sample via an image-forming opticalsystem, and to read that image with a detector; wherein theimage-forming lens in said image-forming optical system is fabricated asa convex lens, on whose flat side is formed an interfering filter forfluorescence.
 8. A biochip reader configured to irradiate excitationlight to a sample, to form an image of fluorescence generated fromfluorescent substances in said sample via an image-forming opticalsystem, and to read that image with a detector; wherein mixing ofexcitation light into the detector side is prevented by mounting a mask,that has approximately the same area as that for the diameter of saidexcitation light beam and masks the excitation light focused with theobjective lens, in said image-forming optical system.
 9. A biochipreader configured to irradiate excitation light to a sample, to form animage of fluorescence generated from fluorescent substances in saidsample via an image-forming optical system, and to read that image witha detector; wherein mixing of excitation light into the detector side isprevented by mounting a mirror, that has approximately the same area asthat for the diameter of said excitation light beam and reflects theexcitation light focused with the objective lens, in said image-formingoptical system.
 10. A transmission type fluorescence reader configuredto irradiate excitation light to a sample, to form an image offluorescence generated from fluorescent substances in said sample via animage-forming optical system, and to read that image with a detector;wherein one barrier filter (or two barrier filters) which act(s) totransmit fluorescence from said fluorescent substances but attenuateexcitation light passing through said sample, is (are) arranged betweenthe sample and objective lens in said image-forming optical system orimmediately before said detector (or in both positions), so that theexcitation light passing through said sample is incident to the barrierfilter at an incident angle of ±5 degrees or less.
 11. A biochip readerthat reads fluorescence generated from genes of each of its cells byirradiating each cell with coherent light such as laser light as theexcitation light; comprising a rotation plate formed so as to berotatable, on which a plurality of microlenses is arranged, atwo-dimensional detector that detects a fluorescence image of saidbiochip using detector elements arranged in a two-dimensional manner,and a barrier filter positioned in the image-forming optical system thatforms an image on the detector surface by detecting fluorescence fromsaid biochip; further configured to rotate said rotation plate, to scansaid biochip with light using excitation light beams individuallycondensed with a said plurality of microlenses, to individuallyirradiate each cell on said biochip, and at the same time to make saidexcitation light to be incident to said detector side incident to saidbarrier filter at an incident angle of ±5 degrees or less.
 12. A biochipreader that irradiates excitation light from a light source to aplurality of cells of the biochip respectively via a plurality ofmicrolenses and reads fluorescence image information from genes to whichfluorescent substances are stuck and which are poured into a saidplurality of cells with a detector; wherein said light source isconfigured to generate excitation light composed of a part of stronglight intensity and another part of weak light intensity, and on saidbiochip, genes of each cell are arranged so that genes are expressedless at the strong light intensity part and are expressed more at theweak light intensity part.
 13. A biochip reader in accordance with claim12, wherein said light source is configured to generate excitation lightthat gives a light intensity distribution in which the intensity isstrong at its center part and weak at the peripheral part.
 14. A biochipreader in accordance with claim 12 or claim 13, wherein a mask that cutsor attenuates part of excitation light is arranged between said lightsource and said sample.
 15. A biochip reader in accordance with any ofclaims 12 to 14, wherein a zoom mechanism for changing the lightintensity distribution of excitation light from said light sourcecorresponding to expression of genes on said biochip, is provided.
 16. Abiochip reader that irradiates excitation light from a light source to aplurality of cells of the biochip respectively via a plurality ofmicrolenses and reads fluorescence image information from genes to whichfluorescent substances are stuck and which are poured into a saidplurality of cells with a detector; wherein said detector is composed ofdetector elements having a characteristic in which output values arelogarithmic to input values.